Genomes and Evolution
Evolutionary Biology Group
Isabel Gordo
Evolutionary change:
-Rate of mutation
-Strenght of natural selection
-level of interaction between mutations - epistasis
Understanding the evolution of any biological system
depends upon understanding each of these mechanisms
Estimates of these parameters in bacteria will have a profound impact on our
understanding of their biology, their diversity, their rate of speciation and in
our health.
Experimental Evolution with bacteria allows us to directly measure these
parameters and to test theoretical predictions about the genetic basis of
adaptive evolution.
Mutation, selection and epistasis
in Escherichia coli
Is there a law governing its adaptation?
R.A. Fisher and a microscope
A random mutation of large effect has much higher
change of being deleterious than of being beneficial
Most beneficial mutations have small effects on fitness
Study of adaptation in E. coli while it is occurring
Genetically modify the bacteria to
measure adaptive mutations as they
get incorporated in the population
time
One adaptive event- selective sweep
Imhof M, Schlotterer C. PNAS 2001
The rate of mutation to beneficial alleles can be as high as 2x10-5
1 in 150 new mutations can be advantageous
Ua=2x10-5 per genome per generation
E(Sa)=0.01
0.45
0.4
Frequency
0.35
0.3
Perfeito et al. Science 2007
0.25
0.2
0.15
0.1
0.05
0
0.007
0.021
0.035
0.049
sa
0.063
0.077
0.091
Fig. 1. Distribution of fitness effects measured in the
populations of Ne=2x104. The grey bars show the distribution of
the measured beneficial mutations
Compatible with Fisher: adaptive mutations of large effect are rarer
Epistasis and evolution of antibiotic resistance
•Mutations confering antibiotic resistance have a benefit
when the drug exists in the environments
•Mutations confering antibiotic resistance have a cost in
drug free environments
If a pathogenic strain is resistant to antibiotic X, which antibiotic
should be administered as a second treatment?
Best combination is that which leads
to the higher cost.
What is the cost of multiple
antibiotic resistance?
Cost of mutation c1
X
Resistant to antibiotic 1
Cost of mutation c2
X
Resistant to antibiotic 2
Cost of mutation 1 & 2 ?
X
X
Resistant to both antibiotics
If c12 = c1+ c2
No epistasis, no interaction e=0
If c12 > c1+ c2
Negative epistasis, high cost e<0
If c12 < c1+ c2
Positive epistasis, low cost e>0
1) Select resistant clones:
rpsL K43N
X
Sequencing
LB with drug
Antibiotics used:
(i) nalidixic acid, which inhibits DNA replication by binding to DNA gyrase;
(ii) rifampin, binds to the b-subunit of RNA polymerase thereby inhibiting transcription;
(iii) streptomycin, binds to the ribosome and inhibits elongation of protein synthesis
2) Make all possible combinations of double resistant clones
Major finding 1
# combinations with positive epistasis
> # with negative epistasis
The cost of double resistance is lower than expected
Major finding 2:
Resistance mutations to a new antibiotic can compensate the cost of
resistance to another antibiotic
"What is true for E. coli is true for the elephant," Jacques Monod
E. coli
Low cost for resistance
mutations X and Y
M. tuberculosis
High frequency of multiple
resistance involving X and Y
Conclusions:
•We estimated that 1 in 150 mutations can be adaptive
•This is the highest estimate ever obtained in a bacteria
•The mean effect of each new beneficial mutations is about 1%.
•The data supports the Fisherian hypothesis that most beneficial mutations
have small effects and those that will fix follow a gamma distribution
Conclusions:
•We estimated that 1 in 150 mutations can be adaptive
•This is the highest estimate ever obtained in a bacteria
•The mean effect of each new beneficial mutations is about 1%.
•The data supports the Fisherian hypothesis that most beneficial mutations
have small effects and those that will fix follow a gamma distribution
• Double antibiotic resistance is less costly than we could a priori
predict
•Very difficult to eliminate resistant bacteria
•Some resistance mutations which are deleterious when in a wildtype background are beneficial (compensatory) when in a genetic
background that contains another resistance => Sign epistasis
Conclusions:
Together these results are the worst nightmare for
the host
and
the best dream for the microbe.
Thanks to:
-Lisete Fernandes (IGC)
-Ana Margarida Sousa(IGC)
-Francisco Dionisio (FCUL)
-Karina Xavier(IGC/ITQB)
-Miguel Godinho Ferreira(IGC)
Lilia Perfeito & Sandra Trindade
Thank you all!!!
Evolutionary questions on mutation
• Is there an optimal mutation rate?
• What is the optimal mutation rate?
R.A. Fisher 1930 “The genetical theory of natural selection”:
optimal U must have an intermediate value
Drake’s Rule
Genomic
mutation rate in
DNA microbes is
~ constant
Drake’s U=0.003
(Drake et al. 1998)
Review by Sniegowski et al (2000)- Pink:RNA viruses (rv, rhinovirus; pv, poliovirus; vsv,
vesicular stomatitis virus; mv, measles virus).
Red: DNA phages M13, T2, T4, and λ.
E. coli (Ec) Saccharomyces cerevisiae (Sc) Neurospora crassa (Nc)
Ce: C. elegans; Dm: Drosophila melanogaster; Mm, Mus musculus; Hs, Homo sapiens